Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Academic Article uri icon


  • Current chemotherapy against Mycobacterium tuberculosis (Mtb), an important human pathogen, requires a multidrug regimen lasting several months. While efforts have been made to optimize therapy by exploiting drugdrug synergies, testing new drug combinations in relevant host environments remains arduous. In particular, host environments profoundly affect the bacterial metabolic state and drug efficacy, limiting the accuracy of predictions based on in vitro assays alone. In this study, we utilized conditional Mtb knockdown mutants of essential genes as an experimentally tractable surrogate for drug treatment and probe the relationship between Mtb carbon metabolism and chemicalgenetic interactions (CGIs). We examined the antitubercular drugs isoniazid, rifampicin, and moxifloxacin and found that CGIs are differentially responsive to the metabolic state, defining both environment-independent and -dependent interactions. Specifically, growth on the in vivorelevant carbon source, cholesterol, reduced rifampicin efficacy by altering mycobacterial cell surface lipid composition. We report that a variety of perturbations in cell wall synthesis pathways restore rifampicin efficacy during growth on cholesterol, and that both environment-independent and cholesterol-dependent in vitro CGIs could be leveraged to enhance bacterial clearance in the mouse infection model. Our findings present an atlas of chemicalgeneticenvironmental interactions that can be used to optimize drugdrug interactions, as well as provide a framework for understanding in vitro correlates of in vivo efficacy.

published proceedings

  • Proc Natl Acad Sci U S A

author list (cited authors)

  • Koh, E., Oluoch, P. O., Ruecker, N., Proulx, M. K., Soni, V., Murphy, K. C., ... Sassetti, C. M.

complete list of authors

  • Koh, Eun-Ik||Oluoch, Peter O||Ruecker, Nadine||Proulx, Megan K||Soni, Vijay||Murphy, Kenan C||Papavinasasundaram, Kadamba||Reames, Charlotte J||Trujillo, Carolina||Zaveri, Anisha||Zimmerman, Matthew D||Aslebagh, Roshanak||Baker, Richard E||Shaffer, Scott A||Guinn, Kristine M||Fitzgerald, Michael||Dartois, Véronique||Ehrt, Sabine||Hung, Deborah T||Ioerger, Thomas R||Rubin, Eric J||Rhee, Kyu Y||Schnappinger, Dirk||Sassetti, Christopher M

publication date

  • April 2022